Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Thalamus segmentation {Disarmed}
by 郑凤莲 15 May '19

15 May '19

External Email - Use Caution Dear Experts, When I used the recent FS version for thalamus segmentation, I have segmented it sucessfully. However, in the .txt file, there are no the volume of lateraldorsal and reticular nuclei. Is there any error in my processing steps? I don't know the reason for this cese. I am looking forward to your reply. Thanks very much in advance. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Download a sample dataset Failed
by Hui Xu 15 May '19

15 May '19

External Email - Use Caution Dear Professors, I began my study of FreeSurfer few days ago. So happy to learn and enjoy data analyses using FreeSurfer. Now, a problem happened when I wanna download a sample dataset which can be used to become familiar with the LME Matlab tools. The download always failed. Please help me to solve this problem. The website is https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels, and please check here "An optional sample dataset which can be used to become familiar with the LME Matlab tools can be found here (485 MB)." This is the sample dataset I wanna download. Many thanks. Hui PhD Candiate, Medical Imaging and Psychology

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Computing measures like area for a custom surface
by Tim Schäfer 15 May '19

15 May '19

External Email - Use Caution Dear list, I have created a custom surface at 50% thickness between the white and pial for my subjects (`mris_expand -thickness lh.white 0.5 lh.graymid`). Is there a way to compute measures like curv and area for this surface using FreeSurfer tools? An example to clarify: I would like to get a file named lh.area.midgray for my new midgray surface, just like I have lh.area and lh.area.pial for the white and pial surfaces, respectively. I have checked the recon-all devtable [1] and it looks like `mris_make_surfaces` is used to compute these measures. But it is not clear to me whether I could use it for a custom surface as well (and if so, how). Best, Tim [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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A Question Regarding Smoothing a Surface
by Maedeh Khalilian 15 May '19

15 May '19

External Email - Use Caution Dear experts, I have a parcellation scheme (an annotation file). Now I wanna smooth the map for better visualization. The command "mri_surf2surf" can do it ,but it doesn't recognize .annot. Now I wonder how to do it. I would appreciate it if u could help me with that. Best wishes, Maedeh,

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Freesurfer 5.3 flags
by Aaron Tanenbaum 14 May '19

14 May '19

External Email - Use Caution Hello freesurfers, Our lab has been using freesurfer 5.3 for a while. We use the following flag when we run the initial recon-all -mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon -custom-tal-atlas TRIO_PIB_NDC_as_mni_average_305 However i have found out that we do not use any of these flags when we have we rerun recon-all after making standard edits. So my question is do any of these flags need to be used when rerun recon-all?

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aparcstats2table
by Alan Francis 14 May '19

14 May '19

External Email - Use Caution Hi Doug: I used the following command: [airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects 100610 --hemi rh --meas thickness --tablefile aparc_stats.txt However, I got an error message: File "/usr/local/freesurfer/stable6/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('ERROR: atleast 1 subject must be provided')? I have used this command on several occasions without any problems, so this is quite puzzling. Could you please help. Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> * *afrancis(a)mclean.harvard.edu <afrancis(a)mclean.harvard.edu>*

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Geometric distortion
by Martin Juneja 14 May '19

14 May '19

External Email - Use Caution Hi experts, I have following question from one of the reviewers regarding recon-all pipeline: *"Was geometric distortion corrected? If not, this should be discussed or mentioned in the study limitation."* I was wondering if the reviewer is referring to following step in the recon-all pipeline. Could you please help me in addressing this concern by the reviewer? Thanks. MJ Cortical Parcellation (-<no>cortparc, -<no>cortparc2) Assigns a neuroanatomical label to each location on the cortical surface. Incorporates both geometric information derived from the cortical model (sulcus and curvature), and neuroanatomical convention. Calls mris_ca_label. -cortparc creates label/?h.aparc.annot, and -cortparc2 creates /label/?h.aparc.a2005s.annot.

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How to obtain the CSF mask
by Yaoshen Yuan 14 May '19

14 May '19

External Email - Use Caution Dear Freesurfer team, I am planning to get the CSF binary mask using Freesurfer. I saw previous discussion about combining several labels in aparc+aseg.nii to create the CSF mask. I am now using Freesurfer v6.0.0. I am wondering does FS now offer a direct mask for CSF using recon-all (I saw gm.mask.mgz and wm.mask.mgz under \mri folder ) or do I still need combine different labels to get the CSF mask? Thank you in advance! Yaoshen Yuan

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Re: [Freesurfer] How can I visualize cortical thickness data on a brain template?
by albertotricker 14 May '19

14 May '19

External Email - Use Caution I hava a data set of 240 patients, 60 Healthy Control, 60 MCI, 60 cMCI and 60 AD, with 429 cortical and subcortical features. 68 of this features are cortical thickness standard desviation features (ie, lh_bankssts_thicknessstd, lh_caudalanteriorcingulate_thicknessstd, … , rh_insula_thicknessstd). I have calculated the average of each of this features for each group (HC, MCI, cMCI, AD) and I want to represent this data over a brain template. For now I am doing this with visbrain, a Python open-source package, but I was wondering if I could do the same with FreeSurfer. I have not found any way to do it in a simple way in the FreeSurfer wiki, but there has to be some way to do it. Thanks you for the help! -- 1/8/1996 Huétor Tájar Alberto Martín Martín _Estudiante de Ingeniería Electrónica Industrial_ UGR _Ingeniero en proceso (de volverse loco)_

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ERROR: flirt in bbr Matlab Execution
by Pfannmoeller, Joerg Peter 14 May '19

14 May '19

Hello, I have a problem with bbregister and the option --init-best. In the current dev version of freesurfer 6 the processing stops with the error message: terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt if I run bbr using Matlab and the Matlab command 'system', where Matlab was started from a terminal in which all FreeSurfer environment variables are set as described on your webpage. However, if I execute the same bbr command from the terminal in which I started Matlab it seemingly runs without any problems. The output files look okay. There is just one output in the log-file which I do not understand: (standard_in) 1: illegal character: K (standard_in) 1: syntax error I got two questions: 1.) Is the run started from the terminal okay? 2.) What do I need to do to get the run started from Matlab to work? The data used worked fine in the stable version for bbregister with fsl flirt initialization in Matlab. However, --init-best did not work in the stable version. In the example discussed here a single slice was registered to the brain anatomy. Here is some information on my operating system: lsb_release -a Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core Can you help me with this issue? Best Joerg

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